Physical Sciences and Mathematics Commons^™

A Biophysical Investigation Of Stability, Ligand Binding, And Iron State Of Cyp102a1, Catherine A. Denning-Jannace

Theses and Dissertations--Chemistry

Cytochrome P450s (CYPs) are cysteine ligated Fe-heme monooxygenases that are found in all domains of life. In mammals, they have a role in xenobiotic metabolism and steroid synthesis, making them a fundamental requirement for survival. In addition, their ability to perform a variety of chemical reactions on an array of substrates makes CYPs highly sought for biotechnical applications such as wastewater remediation, production of potential drug candidates, and creation of drug metabolites. By mutating specific amino acids, these enzymes can be engineered to change their substrate binding profiles and achieve stereo- and regio-specific chemistry. While these mutations are essential to …

Threshold Ionization Spectroscopy And Spin-Orbit Coupling Of Lanthanide Complexes, Yuchen Zhang

Theses and Dissertations--Chemistry

The C-C and C-H bonds have high bond strength and low polarization, which make many small hydrocarbons too inert to react with other molecules under ambient pressure and temperature conditions. Therefore, activation of these bonds is required to convert such small molecules into other value-added chemicals. Among various bond activation methods, metal activation is widely used and reported in the literature, because of its relatively mild reaction conditions and high selectivity.

In this work, Ce atom reactions with several small hydrocarbons are carried out in a pulsed laser vaporization supersonic molecular beam source, and Ce -hydrocarbon species are observed with …

Multi-Modal Medical Imaging Analysis With Modern Neural Networks, Gongbo Liang

Theses and Dissertations--Computer Science

Medical imaging is an important non-invasive tool for diagnostic and treatment purposes in medical practice. However, interpreting medical images is a time consuming and challenging task. Computer-aided diagnosis (CAD) tools have been used in clinical practice to assist medical practitioners in medical imaging analysis since the 1990s. Most of the current generation of CADs are built on conventional computer vision techniques, such as manually defined feature descriptors. Deep convolutional neural networks (CNNs) provide robust end-to-end methods that can automatically learn feature representations. CNNs are a promising building block of next-generation CADs. However, applying CNNs to medical imaging analysis tasks is …

“The Tale Of 3,000 Zircons”: An Investigation Of Grenville Sedimentation In Amazonia Using U/Pb Detrital Zircon Geochronology, Felicia R. Harris

Theses and Dissertations--Earth and Environmental Sciences

The continental collision between Laurentia and Amazonia that generated Rodinia and the Grenville Orogen is proposed to be one of the largest, hottest and longest-lived orogens in Earth history. Subsequent erosion and weathering led to a mountain range’s worth of sediment recycled into clastic systems across North America, otherwise known as the “Great Grenville Sedimentation Event”. The Sunsas orogeny in Amazonia is correlative to the Grenville in North America and is proposed to be the result of final Rodinian collision at 1200-1000 Ma. Despite the connection between the two ranges and the robust sedimentary record in North America, little work …

“Distance Learning” In The Ninth Century?: Micro-Cluster Analysis Of The Epistolary Network Of Alcuin After 796, William James Mattingly

Theses and Dissertations--History

Scholars of eighth- and ninth-century education have assumed that intellectuals did not write works of Scriptural interpretation until that intellectual had a firm foundation in the seven liberal arts.This ensured that anyone who embarked on work of Scriptural interpretation would have the required knowledge and methods to read and interpret Scripture correctly. The potential for theological error and the transmission of those errors was too great unless the interpreter had the requisite training. This dissertation employs computistical methods, specifically the techniques of social network mapping and cluster analysis, to study closely the correspondence of Alcuin, a late-eighth- and early-ninth-century scholar …

Orthogonal Recurrent Neural Networks And Batch Normalization In Deep Neural Networks, Kyle Eric Helfrich

Theses and Dissertations--Mathematics

Despite the recent success of various machine learning techniques, there are still numerous obstacles that must be overcome. One obstacle is known as the vanishing/exploding gradient problem. This problem refers to gradients that either become zero or unbounded. This is a well known problem that commonly occurs in Recurrent Neural Networks (RNNs). In this work we describe how this problem can be mitigated, establish three different architectures that are designed to avoid this issue, and derive update schemes for each architecture. Another portion of this work focuses on the often used technique of batch normalization. Although found to be successful …

Scrollar Invariants Of Tropical Chains Of Loops, Kalila Joelle Sawyer

Theses and Dissertations--Mathematics

We define scrollar invariants of tropical curves with a fixed divisor of rank 1. We examine the behavior of scrollar invariants under specialization, and compute these invariants for a much-studied family of tropical curves. Our examples highlight many parallels between the classical and tropical theories, but also point to some substantive distinctions.

Solutions To Systems Of Equations Over Finite Fields, Rachel Petrik

Theses and Dissertations--Mathematics

This dissertation investigates the existence of solutions to equations over finite fields with an emphasis on diagonal equations. In particular:

1. Given a system of equations, how many solutions are there?
2. In the case of a system of diagonal forms, when does a nontrivial solution exist?

Many results are known that address (1) and (2), such as the classical Chevalley--Warning theorems. With respect to (1), we have improved a recent result of D.R. Heath--Brown, which provides a lower bound on the total number of solutions to a system of polynomials equations. Furthermore, we have demonstrated that several of our lower bounds …

Resource Efficient Design Of Quantum Circuits For Cryptanalysis And Scientific Computing Applications, Edgard Munoz-Coreas

Theses and Dissertations--Electrical and Computer Engineering

Quantum computers offer the potential to extend our abilities to tackle computational problems in fields such as number theory, encryption, search and scientific computation. Up to a superpolynomial speedup has been reported for quantum algorithms in these areas. Motivated by the promise of faster computations, the development of quantum machines has caught the attention of both academics and industry researchers. Quantum machines are now at sizes where implementations of quantum algorithms or their components are now becoming possible. In order to implement quantum algorithms on quantum machines, resource efficient circuits and functional blocks must be designed. In this work, we …

Electrical And Magnetic Transport Properties Of Periodic And Aperiodic Artificial Spin Ice Systems, Justin Woods

Theses and Dissertations--Physics and Astronomy

In recent years, the topic of magnetic frustration in systems and the effect that frustration can have on system dynamics has been a rich environment for study. One such system that lends itself directly to this study are systems of single domain ferromagnetic bars in two dimensions. These ferromagnetic bars can be fabricated from a thin film using current lithography techniques. The bars are fabricated in such a way that their shape anisotropy dictates the magnetization of the bar will be a single domain, Ising-like magnetic moment. These single domain magnetic bars scan be arranged to introduce frustration of their …

Testing Interpretations Of The Displacement Magnitude Of The Teton Fault And Uplift Of The Teton Range, Wyoming With Integrated Flexural-Kinematic And Thermal Modeling, Autumn Helfrich

Theses and Dissertations--Earth and Environmental Sciences

The Teton fault is a range-front normal fault in northwestern Wyoming. Previous estimates of the maximum displacement (D_max) on the Teton fault cover a wide range (2 - 11 km). Discrepancies also exist regarding the slip onset timing, which spans 2 - 13 Ma. To address these discrepancies, the exhumation history of the Teton Range is here investigated using forward flexural-kinematic (Move) and thermal-kinematic (Pecube) models that can be compared with previously reported apatite fission track (AFT) and apatite (U-Th)/He (AHe) ages from Mount Moran, which has been previously hypothesized to represent the …

Quantum Phases And Phase Transitions In Designer Spin Models, Nisheeta Desai

Theses and Dissertations--Physics and Astronomy

This work focuses on numerical studies of quantum spin systems. These simple models are known to exhibit a variety of phases, some of which have no classical counterpart. Phase transitions between them are driven by quantum fluctuations and the unconventional nature of some such transitions make them a fascinating avenue of study.

Quantum Monte Carlo (QMC) is an indispensable tool in the study of these phases and phase transitions in two and higher dimensions. Nevertheless, we are limited by our inability to simulate models that suffer from the infamous sign problem. While the case of S=1/2 has been studied …

The Pion Form Factor And Momentum And Angular Momentum Fractions Of The Proton In Lattice Qcd, Gen Wang

Theses and Dissertations--Physics and Astronomy

Lattice Quantum Chromodynamics (QCD) provides a way to have a precise calculation and a new way of understanding the hadrons from first principles. From this perspective, this dissertation focuses first on a precise calculation of the pion form factor using overlap fermions on six ensembles of 2+1-flavor domain-wall configurations generated by the RBC/UKQCD collaboration with pion masses varying from 137 to 339 MeV. Taking advantage of the fast Fourier transform, low-mode substitution (LMS) and the multi-mass algorithm to access many combinations of source and sink momenta, we have done a simulation with various valence quark masses and with a range …

Theoretical Studies Of C And Cp Violation In $\Eta \To \Pi^+ \Pi^- \Pi^0$ Decay, Jun Shi

Theses and Dissertations--Physics and Astronomy

A violation of mirror symmetry in the $\eta\to\pi^+\pi^-\pi^0$ Dalitz plot has long been recognized as a signal of C and CP violation. In this thesis, we show how the isospin of the underlying C- and CP-violating structures can be reconstructed from their kinematic representation in the Dalitz plot. Our analysis of the most recent experimental data reveals, for the first time, that the C- and CP-violating amplitude with total isospin I = 2 is much more severely suppressed than that with total isospin I = 0.

In searching for C- and CP-violating sources beyond the SM, we enumerate the leading-dimension, …

Effects Of Aperiodicity And Frustration On The Magnetic Properties Of Artificial Quasicrystals, Barry Farmer

Theses and Dissertations--Physics and Astronomy

Quasicrystals have been shown to exhibit physical properties that are dramatically different from their periodic counterparts. A limited number of magnetic quasicrystals have been fabricated and measured, and they do not exhibit long-range magnetic order, which is in direct conflict with simulations that indicate such a state should be accessible. This dissertation adopts a metamaterials approach in which artificial quasicrystals are fabricated and studied with the specific goal of identifying how aperiodicity affects magnetic long-range order. Electron beam lithography techniques were used to pattern magnetic thin films into two types of aperiodic tilings, the Penrose P2, and Ammann-Beenker tilings. SQUID …

Deconvolution Tools For Extracting Insight From Challenging Two-Flavin Systems, Dallas Michael Bell

Theses and Dissertations--Chemistry

Flavoproteins have long been explored for their ubiquity among a number of metabolic and energetic reactions. The flavin cofactor has the inherent benefit of distinct spectral changes associated with redox transitions; however, the double-edged sword is incurred as these distinct signatures overlap and take up much of the UV-vis spectral range. Therefore, it is crucial to create a method to demarcate the expressed redox transitions for studying these systems. The first portion of these studies discusses the creation of a program that deduces spectra for redox transitions in a single-flavin containing model protein: flavodoxin. The latter portions discuss the application …

Estimating Free-Flow Speed With Lidar And Overhead Imagery, Armin Hadzic

Theses and Dissertations--Computer Science

Understanding free-flow speed is fundamental to transportation engineering in order to improve traffic flow, control, and planning. The free-flow speed of a road segment is the average speed of automobiles unaffected by traffic congestion or delay. Collecting speed data across a state is both expensive and time consuming. Some approaches have been presented to estimate speed using geometric road features for certain types of roads in limited environments. However, estimating speed at state scale for varying landscapes, environments, and road qualities has been relegated to manual engineering and expensive sensor networks. This thesis proposes an automated approach for estimating free-flow …

Deep Neural Architectures For End-To-End Relation Extraction, Tung Tran

Theses and Dissertations--Computer Science

The rapid pace of scientific and technological advancements has led to a meteoric growth in knowledge, as evidenced by a sharp increase in the number of scholarly publications in recent years. PubMed, for example, archives more than 30 million biomedical articles across various domains and covers a wide range of topics including medicine, pharmacy, biology, and healthcare. Social media and digital journalism have similarly experienced their own accelerated growth in the age of big data. Hence, there is a compelling need for ways to organize and distill the vast, fragmented body of information (often unstructured in the form of natural …

Interfaces In Lead-Free Tin Perovskite Photovoltaics: An Investigation Of Energetics, Ion Mobility, Surface Modification, And Performance, Alex Boehm

Theses and Dissertations--Chemistry

Halide perovskites have generated tremendous interest as low-cost semiconductors for optoelectronics, such as photovoltaics, lasers, and light emitting diodes due to their extraordinary optical and transport properties. Perovskite photovoltaics in particular have demonstrated a meteoric rise in power conversion efficiencies and drawn considerable interest as a next-generation solar energy technology. The rapid development has centered around lead-based derivatives, and concerns regarding the toxicity of lead has sparked interest in low toxicity and more environmentally friendly perovskite derivatives. In this regime tin (Sn) is regarded as a prominent alternative owing to the ideal bandgap and reduced toxicity exhibited by Sn-halide perovskites. …

Fault Identification On Electrical Transmission Lines Using Artificial Neural Networks, Christopher W. Asbery

Theses and Dissertations--Electrical and Computer Engineering

Transmission lines are designed to transport large amounts of electrical power from the point of generation to the point of consumption. Since transmission lines are built to span over long distances, they are frequently exposed to many different situations that can cause abnormal conditions known as electrical faults. Electrical faults, when isolated, can cripple the transmission system as power flows are directed around these faults therefore leading to other numerous potential issues such as thermal and voltage violations, customer interruptions, or cascading events. When faults occur, protection systems installed near the faulted transmission lines will isolate these faults from the …

Nonparametric Tests Of Lack Of Fit For Multivariate Data, Yan Xu

Theses and Dissertations--Statistics

A common problem in regression analysis (linear or nonlinear) is assessing the lack-of-fit. Existing methods make parametric or semi-parametric assumptions to model the conditional mean or covariance matrices. In this dissertation, we propose fully nonparametric methods that make only additive error assumptions. Our nonparametric approach relies on ideas from nonparametric smoothing to reduce the test of association (lack-of-fit) problem into a nonparametric multivariate analysis of variance. A major problem that arises in this approach is that the key assumptions of independence and constant covariance matrix among the groups will be violated. As a result, the standard asymptotic theory is not …

Laser Ablation In Liquid For The Controlled Production Of Photoluminescent Graphene Quantum Dots And Upconverting Nanoparticles, Rosemary Lynn Calabro

Theses and Dissertations--Chemistry

Photoluminescent­ (PL) nanomaterials play an important role in areas including displays, sensing, solar, photocatalysis, and bio applications. Traditional methods to prepare PL materials suffer many drawbacks such as harsh chemical precursors, complicated synthetic steps, and production of many byproducts. Laser ablation in liquid (LAL) has emerged as a promising alternative to prepare materials that is single-step, fast, uses fewer precursors, produces fewer side products, and has simple purification steps. During LAL, a solid target is irradiated with a pulsed laser source. The laser pulses cause plasma plumes of the target material to form which are cooled, condensed, and can react …

Uncovering Structure-Property Relationships Of Inorganic Nanomaterials Via Transmission Electron Microscopy, Melonie Thomas

Theses and Dissertations--Chemistry

The rapid increase of research in nanoscale devices and nanotechnology in the past few decades has revealed that nanomaterials may possess exceptional properties that are significantly different from the bulk counterpart, due to local rearrangements of the atoms at surfaces and defects. Transmission electron microscopy (TEM) is an indispensable tool when it comes to the characterization of nanomaterials, primarily due to its ability to resolve the local-structure of materials at the atomic-scale. To study dynamic processes, however, regular TEM experiments are inadequate, as they provide only before and after information rather than the real-time data essential to understanding a reaction …

Structure, Surface, And Interfacial Modifications Of Carbon And Supported-Metal Electrodes For Electrochemical Carbon Dioxide Conversion, Namal Wanninayake

Theses and Dissertations--Chemistry

Currently, the global emission of greenhouse CO₂ is over 36 billion tons per year. Consequently, the atmosphere's CO₂ concentrations have exceeded 400 ppm, which is the highest reported in the last three million years. The accumulation of CO₂ is the most critical origin for today's climate change; thus, closing the carbon cycle is vital to reverse the detrimental impacts of climate change. Under this goal, the electrochemical reduction of CO₂ into commodity fuels and chemicals via renewable energy is one of the most promising strategies to recycle CO₂. Despite significant progress made in electrocatalysis, …

Synthesis Of Metal Oxide Surface And Interface Arrays By A Combined Solid-Liquid- Vapor/Vapor-Liquid-Solid Approach, Alexandra J. Riddle

Theses and Dissertations--Chemistry

This project was motivated by an in situ heating experiment in the transmission electron microscope (TEM) in which gold (Au) nanoparticles were observed to dissolve tin dioxide (SnO2) nanowires (NWs) under vacuum. The explanation for this observation was that the high-temperature and low-pressure environment of the TEM caused the reverse reaction of the well-known vapor-liquid-solid (VLS) method commonly used to grow NWs. In the VLS process, a metal catalyst absorbs reactant vapor until it becomes supersaturated. The precipitation of the NW occurs at the liquid-solid interface, which ceases when there is no longer reactant vapor, and the diameter of the …

Structural And Lexical Methods For Auditing Biomedical Terminologies, Rashmie Abeysinghe

Theses and Dissertations--Computer Science

Biomedical terminologies serve as knowledge sources for a wide variety of biomedical applications including information extraction and retrieval, data integration and management, and decision support. Quality issues of biomedical terminologies, if not addressed, could affect all downstream applications that use them as knowledge sources. Therefore, Terminology Quality Assurance (TQA) has become an integral part of the terminology management lifecycle. However, identification of potential quality issues is challenging due to the ever-growing size and complexity of biomedical terminologies. It is time-consuming and labor-intensive to manually audit them and hence, automated TQA methods are highly desirable. In this dissertation, systematic and scalable …

Temporal Data Extraction And Query System For Epilepsy Signal Analysis, Yan Huang

Theses and Dissertations--Computer Science

The 2016 Epilepsy Innovation Institute (Ei2) community survey reported that unpredictability is the most challenging aspect of seizure management. Effective and precise detection, prediction, and localization of epileptic seizures is a fundamental computational challenge. Utilizing epilepsy data from multiple epilepsy monitoring units can enhance the quantity and diversity of datasets, which can lead to more robust epilepsy data analysis tools. The contributions of this dissertation are two-fold. One is the implementation of a temporal query for epilepsy data; the other is the machine learning approach for seizure detection, seizure prediction, and seizure localization. The three key components of our temporal …

Tracing Source Contributions To Assess Spatial Patterns Of Erosion In A Mixed Land Use Environment: Otter Creek Catchment, Fort Knox, Kentucky, Cara Peterman

Theses and Dissertations--Earth and Environmental Sciences

There is an inherent difficulty in predicting source contributions of fine-grained fluvial sediment in mixed land-use watersheds. Over a 56-week period, the spatial and temporal variability in sediment-source contributions and water quality was monitored at three sites along Otter Creek in Hardin and Meade counties, Kentucky (USA). The 203-km² study area drains rural and agricultural lands and includes Fort Knox Army Post’s tracked-vehicle training areas. The main objectives for sediment source apportionment were to 1) identify and differentiate characteristics of civilian and military source soils to Otter Creek and 2) to apportion sediment at locations along Otter Creek to …

Biogeomorphology Of Bedrock Fluvial Systems: Example From Shawnee Run, Kentucky, Usa, Tasnuba Jerin

Theses and Dissertations--Geography

The dynamic interactions between fluvial processes and vegetation vary in different environments and are uncertain in bedrock settings. Bedrock streams are much less studied than alluvial in all aspects, and in many respects act in qualitatively different ways. This research seeks to fill this lacuna by studying bedrock streams from a biogeomorphic perspective. The first part of this research aims to identify the impacts of woody vegetation that may be common to fluvial systems and rocky hillslopes in general, or that may be unique to bedrock channels. A review of the existing literature on biogeomorphology — mostly fluvial and rocky …

A Comparative Analysis Of Reinforcement Learning Applied To Task-Space Reaching With A Robotic Manipulator With And Without Gravity Compensation, Jonathan Fugal

Theses and Dissertations--Electrical and Computer Engineering

Advances in computing power in recent years have facilitated developments in autonomous robotic systems. These robotic systems can be used in prosthetic limbs, wearhouse packaging and sorting, assembly line production, as well as many other applications. Designing these autonomous systems typically requires robotic system and world models (for classical control based strategies) or time consuming and computationally expensive training (for learning based strategies). Often these requirements are difficult to fulfill. There are ways to combine classical control and learning based strategies that can mitigate both requirements. One of these ways is to use a gravity compensated torque control with reinforcement …